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Bioinformatics Advance Access originally published online on May 16, 2006
Bioinformatics 2006 22(15):1838-1845; doi:10.1093/bioinformatics/btl192
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Developing a move-set for protein model refinement

Marc N. Offman , Paul W. Fitzjohn and Paul A. Bates *

Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories London, WC2A 3PX, UK

*To whom correspondence should be addressed.

Motivation: A wide variety of methods for the construction of an atomic model for a given amino acid sequence are known, the more accurate being those that use experimentally determined structures as templates. However, far fewer methods are aimed at refining these models. The approach presented here carefully blends models created by several different means, in an attempt to combine the good quality regions from each into a final, more refined, model.

Results: We describe here a number of refinement operators (collectively, ‘move-set’) that enable a relatively large region of conformational space to be searched. This is used within a genetic algorithm that reshuffles and repacks structural components. The utility of the move-set is demonstrated by introducing a cost function, containing both physical and other components guiding the input structures towards the target structure. We show that our move-set has the potential to improve the conformation of models and that this improvement can be beyond even the best template for some comparative modelling targets.

Availability: The POPULUS software package and the source code are available at http://bmm.cancerresearchuk.org/~offman01/populus.html

Contact: paul.bates{at}cancer.org.uk

Received on March 13, 2006; revised on May 4, 2006; accepted on May 14, 2006

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